procedure so it can be used by program test_set_all_outerm.

Move dummy argument corner of set_all_outerm to last position.

Bug fix in procedure get_snapshot: urc(2) must always be lower than
nlat, even if periodic is true. Fix the same bug in procedure
set_all_outerm: llc(2) >= 1 and urc(2) <= nlat even if periodic is true.

Bug fix in procedure set_all_outerm: the lower bound of dummy argument
ssh is not always 1.

Make script examine_ssh_values.py work for a periodic domain.

Make program test_set_all_outerm work for a periodic
domain. max_radius is now chosen at run-time (we must change it for
a very coarse grid). Add a corresponding test.

In written shapefiles, replace field "area" by field "r_eq_area",
that is radius of disk of equal area. This is a smaller number so it
needs fewer characters, especially for a global coarse grid.

longitude and latitude instead of second longitude and latitude to
compute step. This divides the rounding error on step by a factor nlon
or nlat.

and test_set_all_outerm.

values at longitude boundaries, in case of periodicity.

Add argument "periodic" to procedures get_snapshot and
set_all_outerm. Duplicate values at longitude boundaries in ssh, u, v
if periodic. set_all_outerm can now call local_extrema with periodic
true. In procedure set_all_outerm, we shift the longitudes of outside
points if necessary.

In program test_get_snapshot, define periodic from step and nlon.

internal procedure.

In procedure local_extrema, if periodic, pass arrays "field" and
"extr_map" with a duplicate column at each bound. Then there is no
need to copy to local 3x3 arrays. Add argument my_lbound.

first dimension of input field. So there may be extrema on the borders
and we have to create a private procedure local_extremum.

Added scale option to script plot_snapshot.py.

not six significant decimal digits.

reading and spares some disk space: we can reduce the size of the
field from 20 to 14 characters. We do not loose precision with this
reduction because the order of magnitude of the area is 1e3 km2 or
more so the decimal part of the field was 0. Accordingly, change the
are for a null contour from - 1 to - 1e6 m2.

Bug fix in program test_set_max_speed. No need for width 20 for field "speed".

validity of an eddy depending not only on its amplitude but also its
surface. (Note that, in this version, the component valid is redundant: one
can simply test the component out_cont%n_points.)

amplitude min_amp if the difference between innermost level from
local_extrema and ssh extremum is smaller. This is not only a
performance improvement but also an improvement of results: the
algorithm sometimes finds a contour at just min_amp when before it did
not find any: the bisection algorithm converged just below
min_amp. Also, as a result, if an outermost contour is found, it is
now necessarily of sufficient amplitude.

corner_window for all eddies in a two-dimensional array.

hard-coding them.

Remove component twice of type eddy, no longer needed.

the logic with flat_extr and noise_around is no longer needed.

set_all_outerm: the value of component suff_amp is modified inside the
first batch of get_1_outerm.

>= 0 everywhere outside of procedure local_extrema.

In test Nearby_extr, use output from Get_snapshot_region_1_noise since
we now use suff_amp in extremum shapefile.

than extr_map /= i.

Preparing to remove the coding of sufficient amplitude in extr_map: do
not use anywhere the sign of extr_map, use the component suff_amp of
the type eddy instead.

In program test_successive_overlap, I would rather not use default
values for namelist variables.

Add a larger test for successive_overlap, to have eddies wih
insufficient amplitude in the region.

Stdin to Input. Two input dir provided for in tests.json: $input_dir
and $large_input_dir.

Rename everywhere variable nearby_extr to outside_points to avoid
confusion with function nearby_extr. Rename file "nearby_extr.csv" to
"outside_points.csv".

In procedure nearby_extr, include in the selection extrema with
different sign, even if they do not have sufficient amplitude.

Bug fix in read_eddy: use the value of read attribute to define
e%interpolated.

Bug fix in test_set_max_speed: forgot conversion to rad.

set_all_outerm and in get_snapshot.

define a selection of extrema. Then get their coordinates. This
prepares the way for a more complex selection: taking cylonicity into account.

procedure get_snapshot. The idea is that, in this branch, nearby_extr
will eventually include extrema depending not only on them having
sufficient amplitude but also on their cyclonicity. Both pieces of
information cannot be simply encoded in extr_map. The downside is that
we compute needlessly nearby_extr if e%radius4 == 1 in set_max_speed.

set_max_speed. Abandon the computation with pack_indices, this was
supposed to give the same result than the computation with argwhere
but be faster if not any(extr_map) < 0. I was not sure of that. I
abandon that because I want to eventually remove the coding of
sufficient amplitude in extr_map.

procedure set_all_outerm. The idea is that, in this branch,
nearby_extr will eventually include extrema depending not only on them
having sufficient amplitude but also on their cyclonicity. Both pieces
of information cannot be simply encoded in extr_map.

title lines in "edgelist_1.csv". Add python script reading
"edgelist_1.csv" into a NetworkX graph.